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Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists
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scholarly article
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PubMed
review article
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Europe PubMed Central
title
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists
(English)
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stated in
PubMed
main subject
big data
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author name string
Morgun
series ordinal
1
1 reference
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Crossref
A Yambartsev
series ordinal
2
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stated in
Crossref
L Thomas
series ordinal
3
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Crossref
N Shulzhenko
series ordinal
4
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Crossref
S Ramsey
series ordinal
5
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X Dong
series ordinal
6
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Crossref
language of work or name
English
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stated in
PubMed
publication date
29 April 2015
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PubMed
published in
Bioinformatics and Biology Insights
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volume
9
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PubMed
page(s)
61-74
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PubMed
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Eigengene networks for studying the relationships between co-expression modules
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Microarrays for cancer diagnosis and classification
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
CoXpress: differential co-expression in gene expression data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
A scalable method for integration and functional analysis of multiple microarray datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
The microarray data analysis process: from raw data to biological significance
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
A data integration methodology for systems biology
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Selection of control genes for quantitative RT-PCR based on microarray data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
PRIDE: the proteomics identifications database
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Discovery of meaningful associations in genomic data using partial correlation coefficients
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Whole-genome annotation by using evidence integration in functional-linkage networks
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Characterizing gene sets with FuncAssociate
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
GeneMerge—post-genomic analysis, data mining, and hypothesis testing
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
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29 September 2017
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
29 September 2017
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
2 June 2018
Inferring pathway crosstalk networks using gene set co-expression signatures.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Algorithms to detect multiprotein modularity conserved during evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Controllability of complex networks.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
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27 November 2018
An introduction to causal inference.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
SIRENE: supervised inference of regulatory networks
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
A global pathway crosstalk network
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
NetworkBLAST: comparative analysis of protein networks.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Computing topological parameters of biological networks.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Comparing protein interaction networks via a graph match-and-split algorithm
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Diffusion kernel-based logistic regression models for protein function prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Use of within-array replicate spots for assessing differential expression in microarray experiments.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Finding disease specific alterations in the co-expression of genes.
1 reference
stated in
PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
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27 November 2018
Protein complex prediction via cost-based clustering
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4415676
retrieved
27 November 2018
Guilt-by-association goes global
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25983554
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
The Th1 /Th2 immune-type response of the recurrent aphthous ulceration analyzed by cDNA microarray
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25983554
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Assortative mixing in directed biological networks
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25983554
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Unexpected links reflect the noise in networks.
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25983554
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.4137/BBI.S12467
1 reference
stated in
PubMed
PMC publication ID
4415676
1 reference
stated in
PubMed
PubMed publication ID
25983554
1 reference
stated in
PubMed
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